Whole genome sequencing analysis of Plasmodium vivax using whole genome capture

Vinetz, Joseph Michael; Chuquiyauri, R.; Schork, N.J.; Winzeler, E.A.; Tewhey, R.; Llanos Cuentas, Elmer Alejandro; Bright, A.T.; Ferreira, M.U.; Abeles, S.

dc.contributor.author	Bright, A.T.
dc.contributor.author	Tewhey, R.
dc.contributor.author	Abeles, S.
dc.contributor.author	Chuquiyauri, R.
dc.contributor.author	Llanos Cuentas, Elmer Alejandro
dc.contributor.author	Ferreira, M.U.
dc.contributor.author	Schork, N.J.
dc.contributor.author	Vinetz, Joseph Michael
dc.contributor.author	Winzeler, E.A.
dc.date.accessioned	2022-01-18T19:34:35Z
dc.date.available	2022-01-18T19:34:35Z
dc.date.issued	2012
dc.identifier.uri	https://hdl.handle.net/20.500.12866/11035
dc.description.abstract	Background: Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important human pathogen. Whole genome analysis methods on patient-derived material are thus likely to have a substantial impact on our understanding of P. vivax pathogenesis and epidemiology. For example, it will allow study of the evolution and population biology of the parasite, allow parasite transmission patterns to be characterized, and may facilitate the identification of new drug resistance genes. Because parasitemias are typically low and the parasite cannot be readily cultured, on-site leukocyte depletion of blood samples is typically needed to remove human DNA that may be 1000X more abundant than parasite DNA. These features have precluded the analysis of archived blood samples and require the presence of laboratories in close proximity to the collection of field samples for optimal pre-cryopreservation sample preparation.Results: Here we show that in-solution hybridization capture can be used to extract P. vivax DNA from human contaminating DNA in the laboratory without the need for on-site leukocyte filtration. Using a whole genome capture method, we were able to enrich P. vivax DNA from bulk genomic DNA from less than 0.5% to a median of 55% (range 20%-80%). This level of enrichment allows for efficient analysis of the samples by whole genome sequencing and does not introduce any gross biases into the data. With this method, we obtained greater than 5X coverage across 93% of the P. vivax genome for four P. vivax strains from Iquitos, Peru, which is similar to our results using leukocyte filtration (greater than 5X coverage across 96% ).Conclusion: The whole genome capture technique will enable more efficient whole genome analysis of P. vivax from a larger geographic region and from valuable archived sample collections.	en_US
dc.language.iso	eng
dc.publisher	BioMed Central
dc.relation.ispartofseries	BMC Genomics
dc.rights	info:eu-repo/semantics/restrictedAccess
dc.rights.uri	https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject	Peru	en_US
dc.subject	genetics	en_US
dc.subject	Malaria	en_US
dc.subject	Plasmodium vivax	en_US
dc.subject	DNA, Protozoan	en_US
dc.subject	genome	en_US
dc.subject	Sequence Analysis, DNA	en_US
dc.subject	chemistry	en_US
dc.subject	analytic method	en_US
dc.subject	cell infiltration	en_US
dc.subject	DNA hybridization	en_US
dc.subject	DNA sequence	en_US
dc.subject	feasibility study	en_US
dc.subject	genome analysis	en_US
dc.subject	Genome, Helminth	en_US
dc.subject	genomic DNA	en_US
dc.subject	in solution hybridization capture method	en_US
dc.subject	leukocyte	en_US
dc.subject	Nucleic Acid Hybridization	en_US
dc.subject	sampling	en_US
dc.subject	sequence analysis	en_US
dc.subject	whole genome capture method	en_US
dc.title	Whole genome sequencing analysis of Plasmodium vivax using whole genome capture	en_US
dc.type	info:eu-repo/semantics/article
dc.identifier.doi	https://doi.org/10.1186/1471-2164-13-262
dc.subject.ocde	https://purl.org/pe-repo/ocde/ford#3.01.02
dc.relation.issn	1471-2164

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Whole genome sequencing analysis of Plasmodium vivax using whole genome capture

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